> Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: doubt about OpenMM (Martin Hoefling) > 2. Re: doubt about OpenMM (Thales Kronenberger) > 3. pullf.xvg (Krzysztof Kuczera) > 4. Pull code for Constraint (xu zhijun) > 5. Re: Number of cooredinate in topol.top and solv.gro not > matching (Justin A. Lemkul) > 6. RE: pullf.xvg (Marzinek, Jan) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 02 May 2012 19:31:02 +0200 > From: Martin Hoefling <martin.hoefl...@googlemail.com> > Subject: Re: [gmx-users] doubt about OpenMM > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fa16f56.1010...@googlemail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Am 30.04.2012 19:32, schrieb Thales Kronenberger: > > Hey Folks, > >> SUDO_USER=laboratorio24 >> PWD=/home/laboratorio24/OpenMM4.0-Linux64/python >> File "setup.py", line 165 >> print "%s" % outputString >> ^ >> SyntaxError: invalid syntax >> INSTALLATION FAILED > > which python version are you using? For versions >= 3.0, the above > syntax is not allowed anymore, afair. > > Best > > Martin > > > ------------------------------ > > Message: 2 > Date: Wed, 2 May 2012 14:32:59 -0300 > From: Thales Kronenberger <kronenberg...@gmail.com> > Subject: Re: [gmx-users] doubt about OpenMM > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CA+S5A5ot0cay=1tJu-_iE9Je+roQWP5fz=Xk3T8=vubqvu+...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I have Python 2.6.5 > > 2012/5/2 Martin Hoefling <martin.hoefl...@googlemail.com> > >> Am 30.04.2012 19:32, schrieb Thales Kronenberger: >> >> Hey Folks, >> >> > SUDO_USER=laboratorio24 >> > PWD=/home/laboratorio24/OpenMM4.0-Linux64/python >> > File "setup.py", line 165 >> > print "%s" % outputString >> > ^ >> > SyntaxError: invalid syntax >> > INSTALLATION FAILED >> >> which python version are you using? For versions >= 3.0, the above >> syntax is not allowed anymore, afair. >> >> Best >> >> Martin >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/676d2a14/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 2 May 2012 12:38:29 -0500 > From: Krzysztof Kuczera <kkucz...@ku.edu> > Subject: [gmx-users] pullf.xvg > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fa17115.6000...@ku.edu> > Content-Type: text/plain; charset="ISO-8859-1"; format=flowed > > Could someone please tell me what exactly is printed in the pullf.xvg > file from an umbrella sampling simulation? > Is it the total force acting the COM of the pull group - i.e. force from > regular potential plus the umbrella force or just the unbiased force? > > Krzysztof Kuczera > > -- > Krzysztof Kuczera > Departments of Chemistry and Molecular Biosciences > The University of Kansas > 2010 Malott Hall > Lawrence, KS 66045 > Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu > http://oolung.chem.ku.edu/~kuczera/home.html > > > > > > ------------------------------ > > Message: 4 > Date: Wed, 2 May 2012 10:40:25 -0700 (PDT) > From: xu zhijun <simulatio...@yahoo.com> > Subject: [gmx-users] Pull code for Constraint > To: gmx-users@gromacs.org > Message-ID: > <1335980425.78289.yahoomailclas...@web162001.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I try to pull the small molecule from the bulk solution to the surface by the > Constraint function. > However, it seems that it does not work well. > > Here my part of run parameters about the Constraint in my mdp file > > ############################## > > constraints???? = all-bonds; hbonds; all-bonds > constraint-algorithm???? = Lincs > > pull??????????? = constraint > pull_geometry?? = distance > pull_dim??????? = N N Y > pull_ngroups??? = 1 > pull_group0???? = Surface > pull_group1???? = Protein > pull_nstxout??? = 1000 > pull_nstfout??? = 1000 > pull_rate1????? = -0.001 > pull_init1????? = 1.73331 > ########################## > > Based my understanding, the pull_rate1 is about -0.001/ps. > That means in the pullx.xvg file, the distance shoud be as follows (only the > z-distance shown, time step is 1fs.) > 1.73331 > 1.72231 > 1.72131 > 1.72031 > . > . > However, in my simulation, the results from the simulation is as follow: > 1.73331 > 1.71154 > 1.75043 > 1.73213 > 1.78065 > 1.79769 > 1.84298 > 1.87008 > > It seems some force has been imposed on the pull molecules. > But in the pullf.xvg the force is ZERO. > I used the latest gromacs version, But for the gromacs4.0 it works very well > (works as what I think). > Can someone help me about the issue? > > Thanks a lot > > Jerry > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/97b52262/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Wed, 02 May 2012 13:43:18 -0400 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Number of cooredinate in topol.top and > solv.gro not matching > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4fa17236.3040...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 5/2/12 1:09 PM, Sangita Kachhap wrote: > >>>> I have to do MD simulation of ligand bound membrane protein in lipid >>>> bilayer. >>>> Thus I am doing tutorialfor Protein - Ligand tutorial: >>>> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html >>>> >>>> I have used following command: >>>> >>>> pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc >>>> >>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 >>>> >>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro >>>> >>>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr >>>> >>>> I am getting stuck at last command. Its showing following error: >>>> >>>> Fatal error: >>>> number of coordinates in coordinate file (solv.gro, 33049) >>>> does not match topology (topol.top, 33064) >>>> For more information and tips for troubleshooting, please check the GROMACS >>>> website at http://www.gromacs.org/Documentation/Errors >>>> >>> >>> Did you follow the link? Did you read >>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology >>> ? >>> >>>> {But when I calculate number of atom in topol.top and solv.gro it is same} >>>> >>> >>> That's not possible. >>> >>>> When I checked above http: I got that such type of error may be due to cpp >>>> variable is not properly set in the .mdp file. >>>> But When I locate ccp in my system and add it to .mdp file. >>>> >>>> " >>>> ; LINES STARTING WITH ';' ARE COMMENTS >>>> title = Minimization ; Title of run >>>> cpp =/usr/bin/cpp >>>> ; Parameters describing what to do, when to stop and what to save >>>> " >>>> >>>> Then also it showing same error. >>>> >>>> Please help me to solve this problem. >>>> >>>> I am using gromacs-4.5.5 and installed with fftw-3.3.1 . >>>> >>> >>> The cpp parameter is ignored for all Gromacs versions as of 4.5. >>> >>> Your problem is that you don't have a ligand in your coordinate file. Note >>> that >>> you're off by 15 atoms, which is exactly how many are in the ligand >>> described >>> in >>> the tutorial. Go back and read the instructions closely, as appending the >>> ligand to the protein coordinate file is discussed in detail. >> >> >> >> Thanks for reply >> >> When I am appending ligand from .gro file and generating complex the new .gro >> file newbox.gro do not have ligand. >> >> Command I have used: editconf -f conf.gro -o newbox.gro -bt dodecahedron -d >> 1.0 >> >> I am appending ligand like this at the end of conf.gro >> >> 163ASN HD21 1689 1.029 -0.671 -0.401 >> 163ASN HD22 1690 0.944 -0.584 -0.525 >> 163ASN C 1691 0.621 -0.740 -0.126 >> 163ASN O1 1692 0.624 -0.616 -0.140 >> 163ASN O2 1693 0.683 -0.703 -0.011 >> 1JZ4 C4 1 2.429 -2.412 -0.007 >> 1JZ4 C14 2 2.392 -2.470 -0.139 >> 1JZ4 C13 3 2.246 -2.441 -0.181 >> 1JZ4 C12 4 2.229 -2.519 -0.308 >> 1JZ4 C11 5 2.169 -2.646 -0.295 >> 1JZ4 H11 6 2.135 -2.683 -0.199 >> 1JZ4 C7 7 2.155 -2.721 -0.411 >> 1JZ4 H7 8 2.104 -2.817 -0.407 >> 1JZ4 C8 9 2.207 -2.675 -0.533 >> 1JZ4 H8 10 2.199 -2.738 -0.621 >> 1JZ4 C9 11 2.267 -2.551 -0.545 >> 1JZ4 H9 12 2.306 -2.516 -0.640 >> 1JZ4 C10 13 2.277 -2.473 -0.430 >> 1JZ4 OAB 14 2.341 -2.354 -0.434 >> 1JZ4 HAB 15 2.369 -2.334 -0.528 >> 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 >> 0.00000 >> 0.00000 >> > > Have you correctly incremented the second line of conf.gro to indicate that > more > atoms have been added? Without it, editconf will read the wrong number of > lines > and exclude the ligand. >
Thanks for reply. I have changed line number in conf.gro and now its working. > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 6 > Date: Wed, 2 May 2012 19:08:08 +0000 > From: "Marzinek, Jan" <j.marzine...@imperial.ac.uk> > Subject: RE: [gmx-users] pullf.xvg > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <787e9efeefc7384580812e4ca26d4f4409fe6...@icexch-m4.ic.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf > of > Krzysztof Kuczera [kkucz...@ku.edu] > Sent: Wednesday, May 02, 2012 6:38 PM > To: Discussion list for GROMACS users > Subject: [gmx-users] pullf.xvg > > Could someone please tell me what exactly is printed in the pullf.xvg > file from an umbrella sampling simulation? > Is it the total force acting the COM of the pull group - i.e. force from > regular potential plus the umbrella force or just the unbiased force? > > Krzysztof Kuczera > > > > Each window in umbrella sampling simulation gives you the biased potential > which > is the harmonic potential. The wham allows you to combine all windows by > applying weights and calculating the unbiased potential which requires > calculation of the free enerrgy associated with introducing the harmonic > pontial > (biased). Please, search literature to see equations. > > Jan > > -- > Krzysztof Kuczera > Departments of Chemistry and Molecular Biosciences > The University of Kansas > 2010 Malott Hall > Lawrence, KS 66045 > Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu > http://oolung.chem.ku.edu/~kuczera/home.html > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > > End of gmx-users Digest, Vol 97, Issue 18 > ***************************************** > With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH ______________________________________________________________________ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists